diff --git a/NEWS.md b/NEWS.md index 369c7747..1eb519e0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,8 +2,6 @@ Polished and simplified data import module including a much improved REDCap import module. -- *CHANGE* `default_parsing()` now ensure unique variable names. - # FreesearchR 25.4.1 Focus is on polish and improved ui/ux. diff --git a/R/app_version.R b/R/app_version.R index 9f8ecb9f..bdb01500 100644 --- a/R/app_version.R +++ b/R/app_version.R @@ -1 +1 @@ -app_version <- function()'Version: 25.4.1.250408_1343' +app_version <- function()'Version: 25.4.1.250403_1506' diff --git a/R/data-summary.R b/R/data-summary.R index b0c72eef..b0669581 100644 --- a/R/data-summary.R +++ b/R/data-summary.R @@ -71,11 +71,7 @@ add_sparkline <- function(grid, column = "vals", color.main = "#2a8484", color.s column = column, renderer = function(data) { data_cl <- class(data) - if (all(sapply(data,is.na))){ - type <- "line" - ds <- data.frame(x = NA, y = NA) - horizontal <- FALSE - } else if (identical(data_cl, "factor")) { + if (identical(data_cl, "factor")) { type <- "column" s <- summary(data) ds <- data.frame(x = names(s), y = s) diff --git a/R/helpers.R b/R/helpers.R index b75d7d80..13dcf5d6 100644 --- a/R/helpers.R +++ b/R/helpers.R @@ -213,7 +213,6 @@ default_parsing <- function(data) { name_labels <- lapply(data, \(.x) REDCapCAST::get_attr(.x, attr = "label")) out <- data |> - setNames(make.names(names(data),unique = TRUE)) |> REDCapCAST::parse_data() |> REDCapCAST::as_factor() |> REDCapCAST::numchar2fct(numeric.threshold = 8, character.throshold = 10) |> diff --git a/R/import-file-ext.R b/R/import-file-ext.R index 51736dd8..855c7046 100644 --- a/R/import-file-ext.R +++ b/R/import-file-ext.R @@ -218,8 +218,8 @@ import_file_server <- function(id, shinyWidgets::updatePickerInput( session = session, inputId = "sheet", - selected = selected, - choices = choices + choices = choices, + selected = selected ) datamods:::showUI(paste0("#", ns("sheet-container"))) } else { @@ -291,32 +291,17 @@ import_file_server <- function(id, ) observeEvent(input$see_data, { - tryCatch({ - datamods:::show_data(default_parsing(temporary_rv$data), title = datamods:::i18n("Imported data"), type = show_data_in) - }, - # warning = function(warn) { - # showNotification(warn, type = "warning") - # }, - error = function(err) { - showNotification(err, type = "err") - } - ) + datamods:::show_data(temporary_rv$data, title = datamods:::i18n("Imported data"), type = show_data_in) }) output$table <- toastui::renderDatagrid2({ req(temporary_rv$data) - tryCatch({ toastui::datagrid( - data = setNames(head(temporary_rv$data, 5),make.names(names(temporary_rv$data))), + data = head(temporary_rv$data, 5), theme = "striped", colwidths = "guess", minBodyHeight = 250 ) - }, - error = function(err) { - showNotification(err, type = "err") - } - ) }) observeEvent(input$confirm, { @@ -419,9 +404,9 @@ import_xls <- function(file, sheet, skip, na.strings) { }) |> purrr::reduce(dplyr::full_join) }, - # warning = function(warn) { - # showNotification(paste0(warn), type = "warning") - # }, + warning = function(warn) { + showNotification(paste0(warn), type = "warning") + }, error = function(err) { showNotification(paste0(err), type = "err") } @@ -448,9 +433,9 @@ import_ods <- function(file, sheet, skip, na.strings) { }) |> purrr::reduce(dplyr::full_join) }, - # warning = function(warn) { - # showNotification(paste0(warn), type = "warning") - # }, + warning = function(warn) { + showNotification(paste0(warn), type = "warning") + }, error = function(err) { showNotification(paste0(err), type = "err") } diff --git a/R/redcap_read_shiny_module.R b/R/redcap_read_shiny_module.R index 28003ace..82986dea 100644 --- a/R/redcap_read_shiny_module.R +++ b/R/redcap_read_shiny_module.R @@ -321,7 +321,7 @@ m_redcap_readServer <- function(id) { "Yes, fill missing, non-repeated values" = "yes", "No, leave the data as is" = "no" ), - selected = "no", + selected = "yes", multiple = FALSE ) } diff --git a/inst/apps/FreesearchR/app.R b/inst/apps/FreesearchR/app.R index 15383d99..0c218e76 100644 --- a/inst/apps/FreesearchR/app.R +++ b/inst/apps/FreesearchR/app.R @@ -10,7 +10,7 @@ #### Current file: /Users/au301842/FreesearchR/R//app_version.R ######## -app_version <- function()'Version: 25.4.1.250408_1343' +app_version <- function()'Version: 25.4.1.250403_1506' ######## @@ -2102,11 +2102,7 @@ add_sparkline <- function(grid, column = "vals", color.main = "#2a8484", color.s column = column, renderer = function(data) { data_cl <- class(data) - if (all(sapply(data,is.na))){ - type <- "line" - ds <- data.frame(x = NA, y = NA) - horizontal <- FALSE - } else if (identical(data_cl, "factor")) { + if (identical(data_cl, "factor")) { type <- "column" s <- summary(data) ds <- data.frame(x = names(s), y = s) @@ -2690,7 +2686,6 @@ default_parsing <- function(data) { name_labels <- lapply(data, \(.x) REDCapCAST::get_attr(.x, attr = "label")) out <- data |> - setNames(make.names(names(data),unique = TRUE)) |> REDCapCAST::parse_data() |> REDCapCAST::as_factor() |> REDCapCAST::numchar2fct(numeric.threshold = 8, character.throshold = 10) |> @@ -3096,8 +3091,8 @@ import_file_server <- function(id, shinyWidgets::updatePickerInput( session = session, inputId = "sheet", - selected = selected, - choices = choices + choices = choices, + selected = selected ) datamods:::showUI(paste0("#", ns("sheet-container"))) } else { @@ -3169,32 +3164,17 @@ import_file_server <- function(id, ) observeEvent(input$see_data, { - tryCatch({ - datamods:::show_data(default_parsing(temporary_rv$data), title = datamods:::i18n("Imported data"), type = show_data_in) - }, - # warning = function(warn) { - # showNotification(warn, type = "warning") - # }, - error = function(err) { - showNotification(err, type = "err") - } - ) + datamods:::show_data(temporary_rv$data, title = datamods:::i18n("Imported data"), type = show_data_in) }) output$table <- toastui::renderDatagrid2({ req(temporary_rv$data) - tryCatch({ toastui::datagrid( - data = setNames(head(temporary_rv$data, 5),make.names(names(temporary_rv$data))), + data = head(temporary_rv$data, 5), theme = "striped", colwidths = "guess", minBodyHeight = 250 ) - }, - error = function(err) { - showNotification(err, type = "err") - } - ) }) observeEvent(input$confirm, { @@ -3297,9 +3277,9 @@ import_xls <- function(file, sheet, skip, na.strings) { }) |> purrr::reduce(dplyr::full_join) }, - # warning = function(warn) { - # showNotification(paste0(warn), type = "warning") - # }, + warning = function(warn) { + showNotification(paste0(warn), type = "warning") + }, error = function(err) { showNotification(paste0(err), type = "err") } @@ -3326,9 +3306,9 @@ import_ods <- function(file, sheet, skip, na.strings) { }) |> purrr::reduce(dplyr::full_join) }, - # warning = function(warn) { - # showNotification(paste0(warn), type = "warning") - # }, + warning = function(warn) { + showNotification(paste0(warn), type = "warning") + }, error = function(err) { showNotification(paste0(err), type = "err") } @@ -4525,7 +4505,7 @@ m_redcap_readServer <- function(id) { "Yes, fill missing, non-repeated values" = "yes", "No, leave the data as is" = "no" ), - selected = "no", + selected = "yes", multiple = FALSE ) } diff --git a/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf b/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf index 2cace927..1950a327 100644 --- a/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf +++ b/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf @@ -5,6 +5,6 @@ account: agdamsbo server: shinyapps.io hostUrl: https://api.shinyapps.io/v1 appId: 13611288 -bundleId: 10077795 +bundleId: 10049531 url: https://agdamsbo.shinyapps.io/freesearcheR/ version: 1 diff --git a/vignettes/FreesearchR.Rmd b/vignettes/FreesearchR.Rmd index c675da22..7255cf3b 100644 --- a/vignettes/FreesearchR.Rmd +++ b/vignettes/FreesearchR.Rmd @@ -35,7 +35,7 @@ As a small note, a standalone Windows app version is on the drawing board as wel ## Importing data -Once in the app and in the "**Import**", you have three options available for importing data: file upload, REDCap server export and local or sample data. +Once in the app and in the "*Import*", you have three options available for importing data: file upload, REDCap server export and local or sample data. After choosing a data source, you can set a threshold to filter data be completenes and further manually specify variables to include for analyses. @@ -43,31 +43,20 @@ After choosing a data source, you can set a threshold to filter data be complete Currently several data file formats are supported for easy import (csv, txt, xls(x), ods, rds, dta). If importing workbooks (xls(x) or ods), you are prompted to specify sheet(s) to import. If choosing multiple sheets, these are automatically merged by common variable(s), so please make sure that key variables are correctly named identically. -A notification is posted with error or success. After succesfull import data can be previewed directly by clicking "click to see data" in the notification. - ### REDCap server export -Export data directly from a REDCap server. You need to first generate an API-token ([see these instruction](https://confluence.research.cchmc.org/pages/viewpage.action?pageId=50987698)) in REDCap. Make sure you have the necessary rights to do so. - -Please don't store the API-key on your device unless encrypted or in a keyring, as this may compromise data safety. Log in to your REDCap server and retrieve the token when needed. - -Type the correct webaddress of your REDCap server. - -The module will validate the information and you can click "Connect". - -This will unfold options to preview your data dictionary (the main database metadata), choose fields/variables to download as well as filtering options. ### Local or sample data + ## Evaluate ### Baseline ### Correlation matrix -## Visuals -There are a number of plotting options to visualise different aspects of the data. +## Visualise Below are the available plot types listed. @@ -89,12 +78,16 @@ c("continuous", "dichotomous", "ordinal", "categorical") |> toastui::datagrid(filters=TRUE,theme="striped") ``` + ## Regression + ## Download ### Report + ### Data + ### Code